A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2025-10-28, 12:57 MDT
based on data in:
/nfs/home/rsbg/01_fastq/04_emily_ebel_bulk_midgut_data_eg_RNAseq/HunterPipeline/02_Hisat2/logs
General Statistics
Showing 18/18 rows.
| Sample Name | % Aligned |
|---|---|
| 22_WNV_A_S1 | 44.4% |
| 22_WNV_B_S2 | 46.6% |
| 22_WNV_C_S3 | 36.9% |
| 22_mock_A_S4 | 71.5% |
| 22_mock_B_S5 | 41.0% |
| 22_mock_C_S6 | 14.3% |
| 26_WNV_A_S7 | 15.4% |
| 26_WNV_B_S8 | 13.4% |
| 26_WNV_C_S9 | 17.6% |
| 26_mock_A_S10 | 44.7% |
| 26_mock_B_S11 | 41.4% |
| 26_mock_C_S12 | 17.3% |
| 30_WNV_A_S13 | 62.5% |
| 30_WNV_B_S14 | 54.4% |
| 30_WNV_C_S15 | 57.5% |
| 30_mock_A_S16 | 46.7% |
| 30_mock_B_S17 | 70.1% |
| 30_mock_C_S18 | 68.1% |
Bowtie 2 / HiSAT2
Results from both Bowtie 2 and HISAT2, tools for aligning reads against a reference genome.URL: http://bowtie-bio.sourceforge.net/bowtie2; https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4
Paired-end alignments
This plot shows the number of reads aligning to the reference in different ways.
Please note that single mate alignment counts are halved to tally with pair counts properly.
There are 6 possible types of alignment:
- PE mapped uniquely: Pair has only one occurence in the reference genome.
- PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
- PE one mate mapped uniquely: One read of a pair has one occurence.
- PE multimapped: Pair has multiple occurence.
- PE one mate multimapped: One read of a pair has multiple occurence.
- PE neither mate aligned: Pair has no occurence.
